Whole Genome Sequencing
-
Cohort browser - Genomics - AF frequency and count not the same size as the cohort I built
- Former User of DNAx Community_39
-
Is it expected that some WGS GraphTyper pVCF files have no variants?
- Permanently deleted user
-
How can I identify which subjects have which alleles of rs56041637 in the WGS data? rs56041637 is an intron variant not in the imputed snps. https://www.ncbi.nlm.nih.gov/snp/rs56041637
- Former User of DNAx Community_10
-
How do I load .p.vcf.gz files into the python environment on the spark cluster? Do I need to use dxdata?
- Former User of DNAx Community_4
-
Hi, By whom and how were the helper filer for the 450K exomes generated? Has any filtering been applied for the pVCF or the plink files? Is the release on the RAP from this pipeline? https://www.nature.com/articles/s41586-021-04103-z
- Former User of DNAx Community_79
-
I am wondering where I can find joint calling for whole genome data. For whole exome data there are 3 folders (population level exome OQFE variants) with joint calls in plink, bgen and pvcf format, but I don't see similar folder under whole genome data?
- Permanently deleted user
-
How to use Ensembl Variant Effect Predictor(VEP) on UKB data for GWAS?
- Former User of DNAx Community_24
-
Can I use GLnexus to create a pVCF for all of the females (273k people) in the UKB cohort?
- Former User of DNAx Community_32
-
How can I run regenie step 2 for all 22 chromosomes at once? I would like regenie to spit out a single output file with gwas summary stats for all 22 chromosomes if feasible. Thanks
- Former User of DNAx Community_96
-
cram cache download/internet access from samtools
- Permanently deleted user
-
Are there alignment reports available?
- Permanently deleted user
-
Are the unplaced contigs of Hg38 included in the alignments?
- Permanently deleted user
-
Subsetting by genome
- Former User of DNAx Community_45
-
Hi, can you give me an idea how to proceed with this; I have an existing series of perl scripts (a few thousand lines), to perform variant calling from cram files. Is there anyway I can translate my current approach onto the Dnanexus system? Thanks
- Former User of DNAx Community_80
-
For pVCF files, e.g. GraphTyper SVs is there a list of the genomic positions of the first and last variant in each batch file ?
- Former User of DNAx Community_64
-
Are there any examples of calculating the genetic risk score from different SNPs for a specific disease (e.g., diabetes) on the Research Analysis Platform (RAP)?
- Former User of DNAx Community_14
Didn't find what you were looking for?
New post